Add checksum verification for ENSEMBL sequence and annotation wrappers #36
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Before going further with this, I would like to discuss an issue I have discovered with the current version: Python's Update: It is also possible to retrieve the data files in Python using the urllib module. Then there is no need for using a subprocess and curl. |
| cksum = int(fields[0]) | ||
| filename = fields[2] | ||
| if filename == basename(snakemake.output[0]): | ||
| cksum_local = int(run(["sum", snakemake.output[0]], capture_output=True).stdout.strip().split()[0]) |
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Here, we should use Pythons internal checksum implementation.
| if filename == basename(snakemake.output[0]): | ||
| cksum_local = int(run(["sum", snakemake.output[0]], capture_output=True).stdout.strip().split()[0]) | ||
| if cksum_local == cksum: | ||
| print("CHECKSUM OK: %s" % snakemake.output[0]) |
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| print("CHECKSUM OK: %s" % snakemake.output[0]) | |
| print("CHECKSUM OK", file=sys.stderr) |
| print("CHECKSUM OK: %s" % snakemake.output[0]) | ||
| exit(0) | ||
| else: | ||
| print("CHECKSUM FAILED: %s" % snakemake.output[0]) |
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| print("CHECKSUM FAILED: %s" % snakemake.output[0]) | |
| print("CHECKSUM FAILED:", snakemake.output[0], file=sys.stderr) |
| @@ -2,21 +2,45 @@ | |||
| __copyright__ = "Copyright 2019, Johannes Köster" | |||
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Once this wrapper has been polished, changes should be transferred to the other wrapper in this PR:
johanneskoester
added
the
stale: contribution welcome
Ideally, the checksum() method I've added would be stored separately to avoid redundancy, but I believe this would break the ability of each wrapper to function stand-alone. If there is a way to import common libraries, please let me know.